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Moldia / Lee_2023

All the code described in the Lee et al. (2023) paper
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Assigning barcodes with plp.build_plps, KeyError 'number' #2

Open Sverreg opened 1 year ago

Sverreg commented 1 year ago

The final step of the PLP_Design notebook throws a KeyError. All previous cells ran successfully. In the attached example I get the specific_seqs_final from the file, to avoid having to run the 2hr+ preceding cells again; I hope this is the correct file, it at least results in the same error, which seems to be pandas looking for a column "number" (in Lprobe_Ver2..) that doesn't exist. Lprobe_Ver2.csv was copied from the example directory in this repository.

specific_targets_final.csv

keyerrornumber

Sverreg commented 1 year ago

I managed to run it with the customized option by changing the separator to ; for the L_probe_library read_csv in probedesign.py. Not sure why this file was ; separated, if it happened on my end when downloading and opening (Ubuntu 22.04), or in the original file from the github repo. Still does not run with the start option.

483: sbh=pd.read_csv(L_probe_library, sep=";")

mgcizzu commented 10 months ago

Hi Sverre, I had forgot about this issue, sorry. You're right. I uploaded a new Lprobe file with the corrected format (including the "number" column that was somehow missing from the previous one). Now it should work with all the options. Apologies again for the slow fix. Marco